Read quality filtering and trimming

The function preprocessReads allows to apply predefined or custom read preprocessing functions to all FASTQ files referenced in a SYSargs2 container, such as quality filtering or adapter trimming routines. The paths to the resulting output FASTQ files are stored in the output slot of the SYSargs2 object. The following example performs adapter trimming with the trimLRPatterns function from the Biostrings package. After the trimming step a new targets file is generated (here targets_trim.txt) containing the paths to the trimmed FASTQ files. The new targets file can be used for the next workflow step with an updated SYSargs2 instance, e.g. running the NGS alignments using the trimmed FASTQ files.

Construct SYSargs2 object from cwl and yml param and targets files.

dir_path <- system.file("extdata/cwl/preprocessReads/trim-se", 
    package = "systemPipeR")
trim <- loadWorkflow(targets = targetspath, wf_file = "trim-se.cwl", 
    input_file = "trim-se.yml", dir_path = dir_path)
trim <- renderWF(trim, inputvars = c(FileName = "_FASTQ_PATH1_", 
    SampleName = "_SampleName_"))
preprocessReads(args = trim, Fct = "trimLRPatterns(Rpattern='GCCCGGGTAA', 
    batchsize = 1e+05, overwrite = TRUE, compress = TRUE)
writeTargetsout(x = trim, file = "targets_trimPE.txt", step = 1, 
    new_col = "FileName1", new_col_output_index = 1, overwrite = TRUE)

FASTQ quality report

The following seeFastq and seeFastqPlot functions generate and plot a series of useful quality statistics for a set of FASTQ files including per cycle quality box plots, base proportions, base-level quality trends, relative k-mer diversity, length and occurrence distribution of reads, number of reads above quality cutoffs and mean quality distribution. The results are written to a PDF file named fastqReport.pdf.

fqlist <- seeFastq(fastq = infile1(trim), batchsize = 10000, 
    klength = 8)
pdf("./results/fastqReport.pdf", height = 18, width = 4 * length(fqlist))

Figure 1: FASTQ quality report for 18 samples

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